MIGA2

mitoguardin 2

Basic information

Region (hg38): 9:129036621-129072082

Previous symbols: [ "C9orf54", "FAM73B" ]

Links

ENSG00000148343 ∙ NCBI:84895 ∙ OMIM:616774 ∙ HGNC:23621 ∙ Uniprot:Q7L4E1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MIGA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIGA2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	2

Variants in MIGA2

This is a list of pathogenic ClinVar variants found in the MIGA2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-129040620-C-T		not specified	Likely benign (Oct 22, 2021)
9-129042412-C-T		not specified	Uncertain significance (Jun 18, 2021)
9-129049897-C-T			Benign (Jun 06, 2017)
9-129049921-C-T			Benign (Apr 16, 2018)
9-129059205-C-T		not specified	Uncertain significance (Sep 01, 2021)
9-129060598-C-T		not specified	Uncertain significance (Oct 26, 2021)
9-129060615-C-G		not specified	Uncertain significance (Sep 01, 2021)
9-129068249-G-A		not specified	Uncertain significance (Nov 10, 2021)
9-129069128-T-C		not specified	Uncertain significance (Aug 10, 2021)
9-129070346-C-T		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIGA2	protein_coding	protein_coding	ENST00000358369	15	35462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000296	0.999	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	316	377	0.838	0.0000245	3793
Missense in Polyphen		110	160.37	0.6859		1657
Synonymous	0.0645	173	174	0.994	0.0000122	1242
Loss of Function	2.99	13	31.0	0.419	0.00000158	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000401	0.000399
Ashkenazi Jewish	0.000208	0.000198
East Asian	0.000295	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000190	0.000185
Middle Eastern	0.000295	0.000272
South Asian	0.0000348	0.0000327
Other	0.000178	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of mitochondrial fusion: acts by forming homo- and heterodimers at the mitochondrial outer membrane and facilitating the formation of PLD6/MitoPLD dimers. May act by regulating phospholipid metabolism via PLD6/MitoPLD. {ECO:0000269|PubMed:26711011}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.488
• ghis: 0.467

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Miga2
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; craniofacial phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: mitochondrial fusion;bone development
• Cellular component: mitochondrial outer membrane;integral component of plasma membrane
• Molecular function: protein binding;protein homodimerization activity;protein heterodimerization activity